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Attempting an answer based on the commentary so far, I might hit the nail on the head but some shooting in the dark here!
This sounds quite a bit like some related scenarios I've been hearing about on and off the [equest-users] list. While I have not run into this yet personally, I can assert you are not alone! Whatever the cause(s), SIM "corruption" issues appear new to version 3.65 build 7173 (the most recent version). I understand there are some established ties to when coil capacities are auto-sized (not specified) and improvements to the associated sizing routines, but an update/patch hasn't surfaced yet to resolve the problem.
You can acquire an installer for the previously published version/build (3.65.7163) here: http://doe2.com/download/equest/ I consider build 7163 my "stable" version though I have 7173 installed alongside to explore & take advantage of the new features on occasion. If you're only going to have one installed (today) I'd recommend build 7163, and more specifically I recommend you give switching to 7163 a shot with your current project.
That said, I'm not sure how smoothly continuing your model development in 7163 after starting in 7173 will go. I would suspect major problems if you were using the doe 2.3 engine in 7173, or otherwise still in wizard edits, but I'm not picking up that's the case from the commentary so far. Certainly worth a shot in a separately saved copy if you don't have time to wrestle with the issues.
If you do have the time, I would recommend notifying Jeff Hirsch directly about your situation and sending him a copy of your project input files (pd2/inp/prd-if-occurring): james.j.hirsch@gmail.com . It could be your situation is related to the coil thing and they are already working on a fix, or else you may have stumbled into a case that could help them resolve the bug. If you don't mind sharing your efforts with the public, posting the same files and explaining the context so far to the [equest-users] mailing list will expose your case to more like me who may have the time to toy around and help you work around the current state of things: http://lists.onebuilding.org/listinfo.cgi/equest-users-onebuilding.org
Best of luck!